Variant report

Variant	rs3738687
Chromosome Location	chr1:228565445-228565446
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:228565409..228568928-chr1:228570030..228574294,4	MCF-7	breast:
2	chr1:228458711..228461742-chr1:228563280..228565996,3	MCF-7	breast:
3	chr1:228527728..228529697-chr1:228564611..228569014,3	MCF-7	breast:
4	chr1:228558923..228567970-chr1:228642651..228648934,10	K562	blood:
5	chr1:228563442..228565477-chr1:228583997..228586027,2	MCF-7	breast:
6	chr1:228537844..228541341-chr1:228565200..228567980,3	MCF-7	breast:
7	chr1:228564295..228567691-chr1:228643865..228646471,5	MCF-7	breast:
8	chr1:228564633..228566549-chr1:228674227..228676700,2	MCF-7	breast:
9	chr1:228548661..228550467-chr1:228564169..228566160,2	MCF-7	breast:
10	chr1:228563759..228568804-chr1:228642363..228648543,9	MCF-7	breast:
11	chr1:228564619..228567322-chr1:228586999..228589515,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000168159	Chromatin interaction
ENSG00000181218	Chromatin interaction
ENSG00000154370	Chromatin interaction
ENSG00000154358	Chromatin interaction
ENSG00000196890	Chromatin interaction
ENSG00000270104	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10157289	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10158088	0.84[EUR][1000 genomes]
rs10158354	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10158680	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10916299	0.82[ASN][1000 genomes]
rs10916313	0.80[ASN][1000 genomes]
rs1150917	0.88[ASN][1000 genomes]
rs1150918	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11555960	0.87[EUR][1000 genomes]
rs11581974	0.85[EUR][1000 genomes]
rs11587839	0.80[ASN][1000 genomes]
rs1188473	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1188474	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1188482	0.86[EUR][1000 genomes]
rs1188483	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1188485	0.80[ASN][1000 genomes]
rs1188487	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1188488	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1188489	0.86[EUR][1000 genomes]
rs12027720	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12031395	0.94[EUR][1000 genomes]
rs12060002	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12061490	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12061642	0.83[AFR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12061733	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12065660	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12065815	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12081278	0.81[ASN][1000 genomes]
rs12082349	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12085738	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12089997	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12093491	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12094956	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12096217	0.87[EUR][1000 genomes]
rs12691493	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12725863	0.80[ASN][1000 genomes]
rs12735877	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12751024	0.81[EUR][1000 genomes]
rs12760907	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13373984	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16848470	0.82[ASN][1000 genomes]
rs2230656	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34090141	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34673199	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35055992	0.83[EUR][1000 genomes]
rs35155240	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35553922	0.81[EUR][1000 genomes]
rs35670307	0.81[EUR][1000 genomes]
rs35711644	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3795800	0.82[ASN][1000 genomes]
rs3795810	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3795811	0.87[ASN][1000 genomes]
rs3795814	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4065231	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4581279	0.86[EUR][1000 genomes]
rs474600	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs491670	0.83[EUR][1000 genomes]
rs493950	0.85[EUR][1000 genomes]
rs493954	0.87[EUR][1000 genomes]
rs494154	0.87[EUR][1000 genomes]
rs503203	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs503391	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs505129	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs513467	0.87[EUR][1000 genomes]
rs532465	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs538604	0.85[EUR][1000 genomes]
rs538851	0.83[EUR][1000 genomes]
rs541959	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56174824	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs564309	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56852844	0.81[ASN][1000 genomes]
rs572442	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs573128	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58462432	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61825285	0.82[ASN][1000 genomes]
rs61825312	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61825336	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61825338	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6426501	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6659690	0.80[ASN][1000 genomes]
rs6666241	0.80[ASN][1000 genomes]
rs7513530	0.85[EUR][1000 genomes]
rs7524236	0.80[ASN][1000 genomes]
rs7555386	0.80[ASN][1000 genomes]
rs9787095	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
5	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
6	nsv873267	chr1:228434395-228585837	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv873270	chr1:228442663-228699477	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
8	nsv1009891	chr1:228450763-228742676	Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
9	nsv873274	chr1:228450868-228585837	Strong transcription Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv873275	chr1:228456147-228585837	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
11	nsv517545	chr1:228456147-228685999	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
12	nsv873276	chr1:228456943-228585837	Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
13	nsv1013500	chr1:228459134-228849601	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
14	nsv873278	chr1:228464248-228585837	Strong transcription Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
15	nsv468271	chr1:228464248-228601638	Bivalent Enhancer Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
16	nsv468283	chr1:228464248-228601638	Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
17	nsv468294	chr1:228464248-228601638	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
18	nsv549295	chr1:228464248-228601638	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
19	nsv470780	chr1:228464248-228606965	Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
20	nsv873279	chr1:228494790-228681195	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
21	nsv873280	chr1:228500627-228603029	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
22	nsv873281	chr1:228505739-228656780	Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
23	esv1808261	chr1:228509427-228674518	Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
24	esv2829948	chr1:228509427-228687948	Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
25	nsv508697	chr1:228540037-228622614	Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228540400-228566200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
2	chr1:228541600-228565800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr1:228553200-228566400	Weak transcription	Psoas Muscle	Psoas
4	chr1:228557600-228565600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
5	chr1:228560600-228565600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:228561200-228566000	Genic enhancers	Right Ventricle	heart
7	chr1:228562600-228566200	Weak transcription	Brain Substantia Nigra	brain
8	chr1:228563000-228565600	Weak transcription	Brain Anterior Caudate	brain
9	chr1:228563000-228565600	Weak transcription	Esophagus	oesophagus
10	chr1:228563000-228566400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:228563200-228565600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr1:228563200-228565800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:228563200-228565800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr1:228563200-228565800	Weak transcription	Osteobl	bone
15	chr1:228563200-228566000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:228563200-228566000	Weak transcription	Right Atrium	heart
17	chr1:228563200-228566200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr1:228563200-228566400	Weak transcription	HSMMtube	muscle
19	chr1:228563400-228565600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:228563400-228565600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr1:228563400-228565800	Weak transcription	Brain Hippocampus Middle	brain
22	chr1:228563400-228565800	Weak transcription	Colon Smooth Muscle	Colon
23	chr1:228563400-228566000	Weak transcription	Ovary	ovary
24	chr1:228563400-228566200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:228563400-228566200	Weak transcription	NHLF	lung
26	chr1:228563800-228565600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:228563800-228565800	ZNF genes & repeats	Fetal Stomach	stomach
28	chr1:228563800-228565800	Weak transcription	Gastric	stomach
29	chr1:228564000-228565800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr1:228564200-228565800	Weak transcription	Left Ventricle	heart
31	chr1:228564600-228565800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:228564800-228565600	Enhancers	Spleen	Spleen
33	chr1:228565000-228565600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:228565000-228565600	Enhancers	Fetal Intestine Large	intestine
35	chr1:228565000-228565800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
36	chr1:228565200-228565600	Strong transcription	Fetal Lung	lung
37	chr1:228565200-228565800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr1:228565200-228566600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:228565200-228567200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
40	chr1:228565200-228567400	Enhancers	Fetal Heart	heart
41	chr1:228565400-228565600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
42	chr1:228565400-228565600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr1:228565400-228565600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
44	chr1:228565400-228565600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr1:228565400-228565600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr1:228565400-228565600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr1:228565400-228565600	Enhancers	Primary T cells from cord blood	blood
48	chr1:228565400-228565600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr1:228565400-228565600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:228565400-228565600	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood

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